├── .envrc ├── .github └── workflows │ ├── dev-ci-actions.yaml │ ├── docs-build-deploy.yaml │ ├── latest-tests.yaml │ ├── main-ci-actions.yaml │ ├── pinned-tests.yaml │ ├── publish-package.yaml │ ├── quality-typing-checks.yaml │ └── release-ci-actions.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── CHANGELOG.md ├── LICENSE ├── README.md ├── docs ├── Makefile ├── make.bat └── source │ ├── _static │ ├── PhysicsML_Logo-01.svg │ ├── PhysicsML_Logo_PhyML_logo full dark-cropped.svg │ ├── PhysicsML_Logo_PhyML_logo full dark.svg │ ├── PhysicsML_Logo_PhyML_logo full light-cropped.svg │ ├── PhysicsML_Logo_PhyML_logo full light.svg │ ├── PhysicsML_Logo_PhyML_logo text dark.svg │ └── PhysicsML_Logo_PhyML_logo text light.svg │ ├── conf.py │ ├── index.md │ └── pages │ ├── datasets │ └── qm_datasets.md │ ├── features │ ├── gdb9_trunc.parquet │ ├── how_to_add_reps.md │ └── intro.md │ ├── models │ ├── allegro.md │ ├── ani.md │ ├── egnn.md │ ├── how_to_add_models.md │ ├── intro.md │ ├── mace.md │ ├── nequip.md │ └── tensor_net.md │ ├── philosophy │ ├── molflux.md │ └── philosophy.md │ ├── plugins │ ├── .gitignore │ ├── alanine-dipeptide-truncated.pdb │ ├── ase.md │ └── openmm.md │ ├── structure │ ├── lightning_layer.md │ ├── molflux_layer.md │ ├── physicsml_structure.md │ ├── torch_layer.md │ └── transfer_learning.md │ └── tutorials │ ├── .gitignore │ ├── ani1x_energy_forces_training.md │ ├── ani1x_truncated.parquet │ ├── gdb9_training.md │ ├── gdb9_trunc.parquet │ ├── gdb9_uncertainty.md │ └── transfer_learning.md ├── environment.yaml ├── init_conda_venv.sh ├── init_python_venv.sh ├── noxfile.py ├── pinned-versions ├── 3.10 │ ├── lockfile.ase.txt │ ├── lockfile.core.txt │ ├── lockfile.openeye.txt │ ├── lockfile.openmm.txt │ └── lockfile.rdkit.txt └── 3.11 │ ├── lockfile.ase.txt │ ├── lockfile.core.txt │ ├── lockfile.openeye.txt │ ├── lockfile.openmm.txt │ └── lockfile.rdkit.txt ├── pyproject.toml ├── src └── physicsml │ ├── __init__.py │ ├── backends │ ├── __init__.py │ ├── backend_selector.py │ ├── openeye_backend.py │ └── rdkit_backend.py │ ├── featurisation │ ├── __init__.py │ └── physicsml_features │ │ ├── atom_features.py │ │ ├── bond_features.py │ │ └── physicsml_features.py │ ├── lightning │ ├── __init__.py │ ├── config.py │ ├── datamodule.py │ ├── graph_datasets │ │ ├── __init__.py │ │ ├── graph_dataset.py │ │ ├── neighbourhood_list_torch.py │ │ └── torch_nl_vendored │ │ │ ├── __init__.py │ │ │ ├── geometry.py │ │ │ ├── linked_cell.py │ │ │ ├── naive_impl.py │ │ │ ├── neighbor_list.py │ │ │ ├── timer.py │ │ │ └── utils.py │ ├── losses │ │ ├── __init__.py │ │ ├── construct_loss.py │ │ ├── loss_base.py │ │ ├── masked_mse_loss.py │ │ ├── multitask_losses.py │ │ ├── serial_bce_w_logits_loss.py │ │ ├── stock_losses.py │ │ └── weighted_mse_loss.py │ ├── model.py │ ├── model_uncertainty.py │ ├── module.py │ ├── pre_batching_in_memory.py │ └── pre_batching_on_disk.py │ ├── models │ ├── __init__.py │ ├── allegro │ │ ├── __init__.py │ │ ├── allegro_prism.py │ │ ├── mean_var │ │ │ ├── __init__.py │ │ │ ├── default_configs.py │ │ │ ├── mean_var_allegro_model.py │ │ │ └── mean_var_allegro_module.py │ │ ├── modules │ │ │ ├── __init__.py │ │ │ ├── allegro.py │ │ │ ├── channels.py │ │ │ ├── contract.py │ │ │ ├── cutoffs.py │ │ │ ├── fc.py │ │ │ ├── layout.py │ │ │ ├── linear.py │ │ │ ├── radial.py │ │ │ └── spmm.py │ │ └── supervised │ │ │ ├── __init__.py │ │ │ ├── allegro_model.py │ │ │ ├── allegro_module.py │ │ │ └── default_configs.py │ ├── ani │ │ ├── __init__.py │ │ ├── ani_1_2_defaults.py │ │ ├── ani_datamodule.py │ │ ├── ani_dataset.py │ │ ├── ani_prism.py │ │ ├── config.py │ │ ├── ensemble │ │ │ ├── default_configs.py │ │ │ ├── ensemble_ani_model.py │ │ │ └── ensemble_ani_module.py │ │ ├── mean_var │ │ │ ├── __init__.py │ │ │ ├── default_configs.py │ │ │ ├── mean_var_ani_model.py │ │ │ └── mean_var_ani_module.py │ │ ├── modules │ │ │ ├── __init__.py │ │ │ └── aev.py │ │ └── supervised │ │ │ ├── __init__.py │ │ │ ├── ani_model.py │ │ │ ├── ani_module.py │ │ │ └── default_configs.py │ ├── egnn │ │ ├── __init__.py │ │ ├── adapter │ │ │ ├── __init__.py │ │ │ ├── adapter_egnn_model.py │ │ │ ├── adapter_egnn_module.py │ │ │ ├── adapter_egnn_utils.py │ │ │ └── default_configs.py │ │ ├── egnn_prism.py │ │ ├── egnn_utils.py │ │ ├── mean_var │ │ │ ├── __init__.py │ │ │ ├── default_configs.py │ │ │ ├── mean_var_egnn_model.py │ │ │ └── mean_var_egnn_module.py │ │ ├── multi_graph │ │ │ ├── __init__.py │ │ │ ├── default_configs.py │ │ │ ├── multi_graph_dataloader.py │ │ │ ├── multi_graph_datamodule.py │ │ │ ├── multi_graph_dataset.py │ │ │ ├── multi_graph_egnn_model.py │ │ │ ├── multi_graph_egnn_module.py │ │ │ └── utils.py │ │ ├── ssf │ │ │ ├── __init__.py │ │ │ ├── default_configs.py │ │ │ ├── ssf_egnn_model.py │ │ │ ├── ssf_egnn_module.py │ │ │ └── ssf_egnn_utils.py │ │ └── supervised │ │ │ ├── __init__.py │ │ │ ├── default_configs.py │ │ │ ├── egnn_model.py │ │ │ └── egnn_module.py │ ├── mace │ │ ├── __init__.py │ │ ├── adapter │ │ │ ├── __init__.py │ │ │ ├── adapter_mace_model.py │ │ │ ├── adapter_mace_module.py │ │ │ ├── adapter_mace_utils.py │ │ │ └── default_configs.py │ │ ├── mace_prism.py │ │ ├── mean_var │ │ │ ├── __init__.py │ │ │ ├── default_configs.py │ │ │ ├── mean_var_mace_model.py │ │ │ └── mean_var_mace_module.py │ │ ├── modules │ │ │ ├── __init__.py │ │ │ ├── _activation.py │ │ │ ├── blocks.py │ │ │ ├── cg.py │ │ │ ├── irreps_tools.py │ │ │ ├── mace.py │ │ │ ├── radial.py │ │ │ └── symmetric_contraction.py │ │ ├── ssf │ │ │ ├── __init__.py │ │ │ ├── default_configs.py │ │ │ ├── ssf_mace_model.py │ │ │ ├── ssf_mace_module.py │ │ │ └── ssf_mace_utils.py │ │ └── supervised │ │ │ ├── __init__.py │ │ │ ├── default_configs.py │ │ │ ├── mace_model.py │ │ │ └── mace_module.py │ ├── nequip │ │ ├── __init__.py │ │ ├── adapter │ │ │ ├── __init__.py │ │ │ ├── adapter_nequip_model.py │ │ │ ├── adapter_nequip_module.py │ │ │ ├── adapter_nequip_utils.py │ │ │ └── default_configs.py │ │ ├── mean_var │ │ │ ├── __init__.py │ │ │ ├── default_configs.py │ │ │ ├── mean_var_nequip_model.py │ │ │ └── mean_var_nequip_module.py │ │ ├── modules │ │ │ ├── __init__.py │ │ │ ├── _activation.py │ │ │ ├── _gate.py │ │ │ ├── convnet_layer.py │ │ │ ├── interaction_block.py │ │ │ ├── nequip.py │ │ │ ├── radial.py │ │ │ └── scale_shift.py │ │ ├── nequip_prism.py │ │ ├── ssf │ │ │ ├── __init__.py │ │ │ ├── default_configs.py │ │ │ ├── ssf_nequip_model.py │ │ │ ├── ssf_nequip_module.py │ │ │ └── ssf_nequip_utils.py │ │ └── supervised │ │ │ ├── __init__.py │ │ │ ├── default_configs.py │ │ │ ├── nequip_model.py │ │ │ └── nequip_module.py │ ├── prism.py │ ├── tensor_net │ │ ├── __init__.py │ │ ├── modules │ │ │ ├── __init__.py │ │ │ ├── embedding.py │ │ │ ├── interaction.py │ │ │ ├── output.py │ │ │ └── utils.py │ │ └── supervised │ │ │ ├── __init__.py │ │ │ ├── default_configs.py │ │ │ ├── tensor_net_model.py │ │ │ └── tensor_net_module.py │ └── utils.py │ ├── plugins │ ├── __init__.py │ ├── ase │ │ ├── __init__.py │ │ ├── ase_ani.py │ │ ├── ase_graph.py │ │ ├── calculator.py │ │ └── load.py │ └── openmm │ │ ├── __init__.py │ │ ├── load.py │ │ ├── openmm_ani.py │ │ ├── openmm_base.py │ │ ├── openmm_graph.py │ │ └── physicsml_potential.py │ ├── py.typed │ └── utils.py └── tests ├── __init__.py ├── ase ├── __init__.py ├── conftest.py ├── test_ase_ani.py └── test_ase_graph.py ├── data ├── alanine-dipeptide-truncated.pdb ├── ani1x.h5 ├── ani_model │ ├── featurisation_metadata.json │ ├── model_artefacts │ │ └── module_checkpoint.ckpt │ └── model_config.json ├── egnn_model │ ├── featurisation_metadata.json │ ├── model_artefacts │ │ └── module_checkpoint.ckpt │ └── model_config.json ├── gdb9.csv ├── gdb9.sdf ├── mace_model │ ├── featurisation_metadata.json │ ├── model_artefacts │ │ └── module_checkpoint.ckpt │ └── model_config.json └── nequip_model │ ├── featurisation_metadata.json │ ├── model_artefacts │ └── module_checkpoint.ckpt │ └── model_config.json ├── openeye ├── __init__.py ├── conftest.py ├── core │ ├── __init__.py │ ├── data │ │ ├── __init__.py │ │ ├── test_datamodule.py │ │ └── test_graph_dataset.py │ └── featurisation │ │ ├── __init__.py │ │ └── test_physicsml_featurisation.py └── integration │ ├── __init__.py │ ├── prism │ ├── __init__.py │ └── test_egnn_prism.py │ └── training │ ├── __init__.py │ └── egnn │ ├── __init__.py │ └── test_egnn.py ├── openmm ├── __init__.py ├── conftest.py ├── test_openmm_ani.py ├── test_openmm_egnn.py ├── test_openmm_mace.py ├── test_openmm_nequip.py └── test_openmm_nnp_potential.py └── rdkit ├── __init__.py ├── conftest.py ├── core ├── __init__.py ├── data │ ├── __init__.py │ ├── test_datamodule.py │ └── test_graph_dataset.py └── featurisation │ ├── __init__.py │ └── test_physicsml_featurisation.py └── integration ├── __init__.py ├── prism ├── __init__.py ├── test_allegro_prism.py ├── test_ani_prism.py ├── test_egnn_prism.py ├── test_mace_prism.py └── test_nequip_prism.py └── training ├── __init__.py ├── allegro ├── __init__.py ├── test_allegro_energy_charges.py ├── test_allegro_forces.py ├── test_allegro_mean_var.py └── test_allergo.py ├── ani ├── __init__.py ├── test_ani.py ├── test_ani_ensemble.py ├── test_ani_forces.py └── test_ani_mean_var.py ├── egnn ├── __init__.py ├── test_adapter_egnn.py ├── test_egnn.py ├── test_egnn_energy_charges.py ├── test_egnn_forces.py ├── test_egnn_mean_var.py └── test_ssf_egnn.py ├── mace ├── __init__.py ├── test_adapter_mace.py ├── test_mace.py ├── test_mace_energy_charges.py ├── test_mace_forces.py ├── test_mace_mean_var.py └── test_ssf_mace.py ├── nequip ├── __init__.py ├── test_adapter_nequip.py ├── test_nequip.py ├── test_nequip_energy_charges.py ├── test_nequip_forces.py ├── test_nequip_mean_var.py └── test_ssf_nequip.py └── tensor_net ├── __init__.py ├── test_tensor_net.py ├── test_tensor_net_energy_charges.py └── test_tensor_net_forces.py /.envrc: -------------------------------------------------------------------------------- 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